You're designing a CPU, and you develop a method for how the CPU will decode and execute instructions. You come up with opcodes for all the instructions you want the CPU to use. As a side effect of your decode/execute method, some of the opcodes you didn't specify do other stuff. Maybe they do the same thing as some of the instructions you planned, or maybe they do weird things that seem meaningless and useless.

Either way, those extra opcodes weren't part of your design, and you don't want people using them. Because maybe a future design of your CPU will use those opcodes for something you actually planned, or maybe you'll figure out a more efficient way to decode and execute opcodes which, as a side effect, will change the way those unplanned opcodes work. So you either just don't document those extra opcodes, or you declare them illegal.

Another thing that can happen is that your CPU is buggy, and some of the opcodes don't do what you planned. The Z80 had undocumented (but commonly used) "shift logical left" instructions. These instructions set bit 0 of the operand to 1, which is strange. It's speculated that these were planned to be ordinary shift operations, but the bit 0 to 1 thing was a bug, and so Zilog just decided to leave those instructions undocumented.